ArticleScientific reports2019
A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- Genomic epidemiology reveals geographically structured co-circulation of AFR10 and AFR13Microbial genomics · 2026Article
- Trichosporon austroamericanum Infections among Hospitalized Patients, France, 2022-2024.Emerging infectious diseases · 2025Review
- Genomic and Computational Analysis Unveils Bacteriocin Based Therapeutics against Clinical Mastitis Pathogens in Dairy Cows.Probiotics and antimicrobial proteins · 2025Article
- Article
- WGS-Based Lineage and Antimicrobial Resistance Pattern ofAntibiotics (Basel, Switzerland) · 2022Article
- Comparative Genome Analysis of 33Pathogens (Basel, Switzerland) · 2020Article
- Investigating Major RecurringFrontiers in cellular and infection microbiology · 2020Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing is increasingly adopted in clinical settings to identify pathogen transmissions, though largely as a retrospective tool. Prospective monitoring, in which samples are continuously added and compared to previous samples, can generate more actionable information. To enable prospective pathogen comparison, genomic relatedness metrics based on single-nucleotide differences must be consistent across time, efficient to compute and reliable for a large variety of samples. The choice of genomic regions to compare, i.e., the core genome, is critical to obtain a good metric. We propose a novel core genome method that selects conserved sequences in the reference genome by comparing its k-mer content to that of publicly available genome assemblies. The conserved-sequence genome is sample set-independent, which enables prospective pathogen monitoring. Based on clinical data sets of 3436 S. aureus, 1362 K. pneumoniae and 348 E. faecium samples, ROC curves demonstrate that the conserved-sequence genome disambiguates same-patient samples better than a core genome consisting of conserved genes. The conserved-sequence genome confirms outbreak samples with high sensitivity: in a set of 2335 S. aureus samples, it correctly identifies 44 out of 44 known outbreak samples, whereas the conserved-gene method confirms 38 known outbreak samples.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.